Xenbase: a Xenopus biology and genomics resource

@article{Bowes2008XenbaseAX,
  title={Xenbase: a Xenopus biology and genomics resource},
  author={Jeff B. Bowes and Kevin A. Snyder and Erik Segerdell and Ross Gibb and Chris Jarabek and Etienne Noumen and Nicolas Pollet and Peter D. Vize},
  journal={Nucleic Acids Research},
  year={2008},
  volume={36},
  pages={D761 - D767}
}
Xenbase (www.xenbase.org) is a model organism database integrating a diverse array of biological and genomic data on the frogs, Xenopus laevis and Xenopus (Silurana) tropicalis. Data is collected from other databases, high-throughput screens and the scientific literature and integrated into a number of database modules covering subjects such as community, literature, gene and genomic analysis. Gene pages are automatically assembled from data piped from the Entrez Gene, Gurdon Institute, JGI… 
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Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.
TLDR
This chapter provides a full description of the many features of Xenbase, and offers a guide on how to use various tools to perform a variety of common tasks such as identifying nucleic acid or protein sequences, finding gene expression patterns for specific genes, stages or tissues, identifying literature on a specific gene or tissue, locating useful reagents and downloading extensive content.
Xenbase: expansion and updates of the Xenopus model organism database
Xenbase (http://www.xenbase.org) is a model organism database that provides genomic, molecular, cellular and developmental biology content to biomedical researchers working with the frog, Xenopus and…
Xenbase: gene expression and improved integration
Xenbase (www.xenbase.org), the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is the principal centralized resource of genomic, development data and community information…
Xenbase: a genomic, epigenomic and transcriptomic model organism database
Abstract Xenbase (www.xenbase.org) is an online resource for researchers utilizing Xenopus laevis and Xenopus tropicalis, and for biomedical scientists seeking access to data generated with these…
An ontology for Xenopus anatomy and development
TLDR
A Xenopus anatomical ontology is constructed that represents the lineage of tissues and the timing of their development and will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
A comparative gene expression database for invertebrates
TLDR
This database is the first web-based comparative gene expression database for invertebrates that allows species-specific as well as cross-species gene expression comparisons and enables a quick identification of putative syn-expression groups that can be used to initiate gene regulatory network (GRN) projects.
Xenopus genomic data and browser resources.
GEISHA: an evolving gene expression resource for the chicken embryo
TLDR
Modifications to GEISHA (Gallus Expression In Situ Hybridization Analysis), an in situ hybridization gene expression and genomic resource for the chicken embryo, are described that enhance its utility to users.
Resources and transgenesis techniques for functional genomics in Xenopus
TLDR
Effective use of resources and techniques will help to reveal the overall picture of the complex wiring of gene regulatory networks that control vertebrate development.
Navigating the Xenopus tropicalis genome.
  • I. Blitz
  • Biology
    Methods in molecular biology
  • 2012
TLDR
This chapter provides a step-by-step guide for the novice to finding genes of interest in the current genome assembly, supplemented with detailed notes to improve understanding.
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